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The primary differentiation event during mammalian development occurs at the blastocyst stage and leads to the delineation of the inner cell mass (ICM) and the trophectoderm (TE). We provide the first global mRNA expression data from immunosurgically dissected ICM cells, TE cells, and intact human blastocysts. Using a cDNA microarray composed of 15,529 cDNAs from known and novel genes, we identify marker transcripts specific to the ICM (e.g.,  OCT4 / POU5F1 ,  NANOG ,  HMGB1 , and  DPPA5 ) and TE (e.g.,  CDX2, ATP1B3, SFN , and  IPL ), in addition to novel ICM‐ and TE‐specific expressed sequence tags. The expression patterns suggest that the emergence of pluripotent ICM and TE cell lineages from the morula is controlled by metabolic and signaling pathways, which include  inter alia , WNT, mitogen‐activated protein kinase, transforming growth factor‐beta, NOTCH, integrin‐mediated cell adhesion, phosphatidylinositol 3‐kinase, and apoptosis. These data enhance our understanding of the first step in human cellular differentiation and, hence, the derivation of both embryonic stem cells and trophoblastic stem cells from these lineages.

Primary Differentiation in the Human Blastocyst: Comparative Molecular Portraits of Inner Cell Mass and Trophectoderm Cells